Generated by Cython 0.19 on Wed Sep 11 16:25:22 2013

Raw output: water_algorithm_cython.c

 1: #cython: wraparound=False

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 2: #cython: nonecheck=False

 3: #cython: infer_types=True

 4: #cython: boundscheck=False

 5: #cython: c_line_in_traceback=False

 6: import numpy as np

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 7: cimport numpy as np

 8: np.import_array()

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 * import math
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 9: import scipy

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 10: import math

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 11: cimport cython

 12: 

 13: import ase

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 * import os
 * 
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 14: import os

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 * 
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 15: 

 16: 

 17: #from mpi4py import MPI

 18: from mpi4py cimport MPI

 19: from mpi4py cimport mpi_c

 20: from time import time

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 * from mpi4py cimport mpi_c
 * from time import time             # <<<<<<<<<<<<<<
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 21: #from result_group_cython import ResultGroup, merge_groups

 22: from .result_group_cython cimport ResultGroup, merge_groups

 23: from .graph_invariants_cython cimport get_invariants, Invariant, InvariantTerm, print_invariants, initialize_new_indexing

 24: from help_methods import *

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 * from .graph_invariants_cython cimport get_invariants, Invariant, InvariantTerm, print_invariants, initialize_new_indexing
 * from help_methods import *             # <<<<<<<<<<<<<<
 * 
 * from .symmetries.symmetry_operation_cython cimport SymmetryOperation, do_symmetry_operation_filtering, remove_earlier_found, mark_earlier_found, all_found, get_sub_symmetry_level_improved
 */
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 25: 

 26: from .symmetries.symmetry_operation_cython cimport SymmetryOperation, do_symmetry_operation_filtering, remove_earlier_found, mark_earlier_found, all_found, get_sub_symmetry_level_improved

 27: from .symmetries.self_symmetry_group_cython cimport SelfSymmetryGroup

 28: from .symmetries.interface_cython cimport find_symmetry_operations, print_symmetry_operations

 29: from symmetries.interface_cython import get_moments_of_inertia, get_closest_positions

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 * from .symmetries.self_symmetry_group_cython cimport SelfSymmetryGroup
 * from .symmetries.interface_cython cimport find_symmetry_operations, print_symmetry_operations
 * from symmetries.interface_cython import get_moments_of_inertia, get_closest_positions             # <<<<<<<<<<<<<<
 * from cpython cimport bool
 * 
 */
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 30: from cpython cimport bool

 31: 

 32: DTYPE = np.uint8

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 33: DTYPE2 = np.int8

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 34: DTYPE4 = np.float

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 35: cdef MPI.Comm comm = MPI.COMM_WORLD

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 37: cdef public unsigned char rank = comm.Get_rank()

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 38: 

 39: cdef class WaterAlgorithm:

/* "water_algorithm_cython.pyx":39
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 *     def __init__(self, filename=""):
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 175: 

 176:     cdef void load_invariants(self):

/* "water_algorithm_cython.pyx":176
 *         return wo
 * 
 *     cdef void load_invariants(self):             # <<<<<<<<<<<<<<
 *         """
 *             Loads graph invariants to the graph_invariants parameter of WaterAlgorithm object (self).
 */

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 177:         """

 178:             Loads graph invariants to the graph_invariants parameter of WaterAlgorithm object (self).

 179:             The actual method are located at graph_invariants_cython -module.

 180:         """

 181:         cdef list symmetry_operations = self.symmetry_operations

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 182:         cdef int i, N = len(symmetry_operations)

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 183:         cdef SymmetryOperation symmetry_operation

 184:         cdef dict conversion_table

 185:         cdef list gi

 186:         if self.symmetry_operations == None or len(self.symmetry_operations) <= 1:

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 187:             self.graph_invariants == None

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 *             self.do_symmetry_check = np.zeros(len(self.oxygen_coordinates), dtype=DTYPE)
 *         if rank == 0:
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 188:             self.do_symmetry_check = np.zeros(len(self.oxygen_coordinates), dtype=DTYPE)

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 189:         if rank == 0:

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 *             self.graph_invariants == None
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 190:             #for i from 0 <= i < N:

 191:             #    symmetry_operation = symmetry_operations[i]

 192:             #    symmetry_operation.get_symbolic_bond_variable_matrix(self.nearest_neighbors_nos, self)

 193:             #print self.get_folder()

 194:             gi = get_invariants(self.symmetry_operations,  self.nearest_neighbors_nos, True, False, self.get_folder(), False, self, self.invariant_count)

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 *             #    symmetry_operation.get_symbolic_bond_variable_matrix(self.nearest_neighbors_nos, self)
 *             #print self.get_folder()
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 198: 

 199:             conversion_table = get_index_conversion_table(self.nearest_neighbors_nos)

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 * 
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 200:             initialize_new_indexing(conversion_table, gi)

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 231: 

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 *     cdef void initialize_symmetry_operations(self):             # <<<<<<<<<<<<<<
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 234:         """

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 241:         cdef SymmetryOperation sop

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 247:             print "Time used in symmetry operation loading %f" % (time() - s)

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 248:             print "Found %i symmetry operations" % len(so)

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 *             so, primitive_symmetry_operations, translation_operations = find_symmetry_operations(oxygens, error_tolerance)
 *             print "Time used in symmetry operation loading %f" % (time() - s)
 *             print "Found %i symmetry operations" % len(so)             # <<<<<<<<<<<<<<
 *             #so = remove_equals(so, debug)
 *         else:
 */
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 249:             #so = remove_equals(so, debug)

 250:         else:

 251:             so = Noner

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 *         else:
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 252:             primitive_symmetry_operations = None

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 *             translation_operations = None
 *         if size > 1:
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 253:             translation_operations = None

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 *         if size > 1:
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 254:         if size > 1:

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 *             self.symmetry_operations = comm.bcast(so,  root=0)
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 255:             self.symmetry_operations = comm.bcast(so,  root=0)

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 256:             self.primitive_symmetry_operations = comm.bcast(primitive_symmetry_operations,  root=0)

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 258:         else:

 259:             self.symmetry_operations = so

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 260:             self.primitive_symmetry_operations = primitive_symmetry_operations

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 261:             self.translation_operations = translation_operations

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 *             self.translation_operations = translation_operations             # <<<<<<<<<<<<<<
 * 
 *     cdef np.ndarray[DTYPE2_t, ndim=2] get_symmetries(self, np.ndarray[DTYPE2_t, ndim=1] result, np.ndarray[DTYPE_t, ndim=3] neareast_neighbors_nos, list symmetry_operations):
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 262: 

 263:     cdef np.ndarray[DTYPE2_t, ndim=2] get_symmetries(self, np.ndarray[DTYPE2_t, ndim=1] result, np.ndarray[DTYPE_t, ndim=3] neareast_neighbors_nos, list symmetry_operations):

/* "water_algorithm_cython.pyx":263
 *             self.translation_operations = translation_operations
 * 
 *     cdef np.ndarray[DTYPE2_t, ndim=2] get_symmetries(self, np.ndarray[DTYPE2_t, ndim=1] result, np.ndarray[DTYPE_t, ndim=3] neareast_neighbors_nos, list symmetry_operations):             # <<<<<<<<<<<<<<
 *         """
 *             DEPRECATED!
 */

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 264:         """

 265:             DEPRECATED!

 266:             Loads the symmetries of given water orientations (result)

 267:             Parameters:

 268:                 result               : the water orientations of the given result

 269:                 nearest_neighbors_nos: the nearest neighbor nos of all water molecules

 270:                 symmetry_operations  : the SymmetryOperation objects in a python list

 271:             Returns the symmetries in a two dimensional numpy array

 272: 

 273:         """

 274:         cdef np.ndarray[DTYPE2_t, ndim=2] symmetries = np.zeros((len(symmetry_operations), result.shape[0]), dtype=DTYPE2)

  /* "water_algorithm_cython.pyx":274
 * 
 *         """
 *         cdef np.ndarray[DTYPE2_t, ndim=2] symmetries = np.zeros((len(symmetry_operations), result.shape[0]), dtype=DTYPE2)             # <<<<<<<<<<<<<<
 *         cdef np.ndarray[DTYPE2_t, ndim=1] symmetry
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 285: 

 286:         #print "Symmetries count %i" % len(symmetries)

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 289: 

 290: 

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 370:             additional_atoms = None

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